Computational Approach to Target SARS-CoV-2 Proteins Using Bioactives Derived from Nerium indicum

Department of Biotechnology, K.S.Rangasamy College of Technology, Tiruchengode, Tamil Nadu, India.

^* Corresponding author: sidhrazameer@gmail.com

Abstract

SARS-CoV-2 spreads through inhalation or contact with infected individuals, with its receptor-binding domain (RBD) facilitating cell entry and causing severe effects. In order to identify a better ailment for this disease, the current study has been made using In-silico tools to predict the interaction of SARS-CoV-2 with natural ligand C-1: N-(4-Hydroxyphenyl)-2-methoxy-2-phenyl-acetamide and C-2: N-(4-Hydroxy-phenyl)-2-phenyl-N-phenylacetyl-acetamide of Nerium indicum as it is concerned with the antiviral property. The target proteins such as Glycoprotein (2GHV), Spike S3 (6LVN) and Protease (5RE5, 5RE8, 5RE9, 5REA, 5REB, 5REE, 5REF, 5REK) were docked against ligands. The results reveals that C-1 and C-2 has the high binding from -4.2 Kcal/mol to -8.1 Kcal/mol than the standard (Fingolimod). The protein 5REA has a highest binding affinity of -8.1 Kcal/ mol with C-2, indicating significant potential for interaction. Further, Molecular Simulation studies were conducted to determine the stability of proteins based on physiological conditions such as potential, temperature, pressure and density. The obtained values ranging from -2.20971E+06 kJ/mol to -1.55E+11 kJ/mol, 299.943 K to 299.68 K, 3.25424 bar to -7.26344 bar to and 1014.98 kg/m³ to 1012.33 kg/m³ determines the flexibility of protein structures and proves that the N. indicum compounds can be a potential drug against SARS-CoV-2.